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- EMDB-12875: The archaellum of Methanocaldococcus villosus -

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Basic information

Entry
Database: EMDB / ID: EMD-12875
TitleThe archaellum of Methanocaldococcus villosus
Map data
Sample
  • Complex: Archaellum
    • Protein or peptide: Archaellin
    • Protein or peptide: Archaellin
  • Ligand: CALCIUM ION
  • Ligand: UNKNOWN LIGAND
KeywordsArchaellum / archaellin / Methanocaldococcus villosus / cryoEM / helical reconstruction / PROTEIN FIBRIL
Biological speciesMethanocaldococcus villosus (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsIsupov M / Gambelli L
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)109784 United Kingdom
Citation
Journal: Nat Commun / Year: 2022
Title: An archaellum filament composed of two alternating subunits.
Authors: Lavinia Gambelli / Michail N Isupov / Rebecca Conners / Mathew McLaren / Annett Bellack / Vicki Gold / Reinhard Rachel / Bertram Daum /
Abstract: Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of ...Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. In many species, several archaellin homologs are encoded in the same operon; however, previous structural studies indicated that archaellum filaments mainly consist of only one protein species. Here, we use electron cryo-microscopy to elucidate the structure of the archaellum from Methanocaldococcus villosus at 3.08 Å resolution. The filament is composed of two alternating archaellins, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify structural elements that may contribute to the filament's flexibility.
#1: Journal: Faraday Disc.Chem.Soc / Year: 2022
Title: Escaping the symmetry trap in helical reconstruction
Authors: Gambelli L / Isupov MN / Daum B
History
DepositionMay 5, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.325
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.325
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ofq
  • Surface level: 0.325
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ofq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12875.png

Downloads & links

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Map

FileDownload / File: emd_12875.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.325 / Movie #1: 0.325
Minimum - Maximum-0.00037812628 - 2.0726879
Average (Standard dev.)0.020517845 (±0.06978854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 355.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z355.840355.840355.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0002.0730.021

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Supplemental data

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Sample components

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Entire : Archaellum

EntireName: Archaellum
Components
  • Complex: Archaellum
    • Protein or peptide: Archaellin
    • Protein or peptide: Archaellin
  • Ligand: CALCIUM ION
  • Ligand: UNKNOWN LIGAND

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Supramolecule #1: Archaellum

SupramoleculeName: Archaellum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methanocaldococcus villosus (archaea)

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Macromolecule #1: Archaellin

MacromoleculeName: Archaellin / type: protein_or_peptide / ID: 1 / Number of copies: 23 / Enantiomer: LEVO
Source (natural)Organism: Methanocaldococcus villosus (archaea)
Molecular weightTheoretical: 22.084279 KDa
Recombinant expressionOrganism: Methanocaldococcus villosus (archaea)
SequenceString: AIGIGTLIIF IAMVLVAAVA AAVLINTSGF LQQKAMATGK ESTEQVASGL LCSGVTGHYV KNKGIDRIVI YITPNAGSAP IDLKQCKLF LMYDGKAVSL NFSKYDTNTV GDFTNGIKDI FNTTVVKWNN ADATSFVVVA LQDDDKSLLT NAVINKGDLA G VLVNVSAA ...String:
AIGIGTLIIF IAMVLVAAVA AAVLINTSGF LQQKAMATGK ESTEQVASGL LCSGVTGHYV KNKGIDRIVI YITPNAGSAP IDLKQCKLF LMYDGKAVSL NFSKYDTNTV GDFTNGIKDI FNTTVVKWNN ADATSFVVVA LQDDDKSLLT NAVINKGDLA G VLVNVSAA FGKHVGTRER VSGYLQPEFG APAVIEFTTP AAFTSDVIEL Q

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Macromolecule #2: Archaellin

MacromoleculeName: Archaellin / type: protein_or_peptide / ID: 2 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Methanocaldococcus villosus (archaea)
Molecular weightTheoretical: 22.273643 KDa
Recombinant expressionOrganism: Methanocaldococcus villosus (archaea)
SequenceString: AIGIGTLIIF IAMVLVAAVA AAVLINTSGF LQQKAMATGK ESTEQVASGL QVIRVLGNHS GGKINWLAVL ISPNAGSAPI DLSQATVMI TDGTHKVIAK YNSTFFNGTL KNGGSIFEAK YNNTTALKPL FDDLPATAFG IVVLQDADTS CSKDTPVINK G DIVAICLN ...String:
AIGIGTLIIF IAMVLVAAVA AAVLINTSGF LQQKAMATGK ESTEQVASGL QVIRVLGNHS GGKINWLAVL ISPNAGSAPI DLSQATVMI TDGTHKVIAK YNSTFFNGTL KNGGSIFEAK YNNTTALKPL FDDLPATAFG IVVLQDADTS CSKDTPVINK G DIVAICLN VSNTLNLKPR TKVTGAVIPE FGAPAVISFT TPATYLDTQH IIELQ

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 45 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 4 / Number of copies: 804 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7 / Component - Concentration: 5.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HEPES
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK III / Details: blotting time of 4 sec, -1 blot force.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2795 / Average exposure time: 1.0 sec. / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 2.7 mm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 33.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -71.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Software - details: Helical Refinement (BETA) / Number images used: 399178
Segment selectionNumber selected: 929165 / Software - Name: EMAN2 / Software - details: e2boxer.py
Startup modelType of model: OTHER
Details: Initial model was done creating a cylinder as by instructions in https://www3.mrc-lmb.cam.ac.uk/relion//index.php?title=Helical_processing
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5o4u


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-7ofq:
The archaellum of Methanocaldococcus villosus

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